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Origins of RNA - a challenge for evolution

Good morning R.R.S. I thought I would post a topic that has been on my mind for a long time.

My recent search for understanding has led me to DNA.

It seems evident to me that DNA is the basis for life on Earth. The single code for life. Furthermore, It seems that evolution is the origin for different types of life on Earth. The common thread between life's origin and life's evolution seems to be DNA. It appears to me that this explanation seems accurate in spite of being very brief. Operating from this understanding, I have deep concerns about the origin of DNA.

[My understanding of things said here after is very limited. I have not studied chemistry or biology beyond freshman college level]

RNA is said to be the building blocks of DNA. That is explanation is all good and well. But where did RNA come from? I just finished reading a chapter in Vital Dust about this very issue and got a very disheartening answer to this question. The general opinion, although disputed among some chemists, is that RNA's origin is completely derived from chance. Not incremental stackings of chance of events, but as it appears, complete sudden chance during early non-life-sustaining Earth.

My question does have evolution as evidence for the non-existence of God debunking underpinnings, but I don't know if I can make a strong case between the lack of knowing the origin of RNA, to the debunking of all of evolutionary evidence. The envisioning I have of how RNA could possibly undermine evolution is because DNA is taken for granted in evolution and not considered derived from sudden chance. (If Mr. Dawkins does address DNA/RNA's origin and I just haven't read it, please let me know what he said.) As Mr. Dawkins points out in that documentary on evolution from BBC, evolution is not sudden chance, but slight chance modifications stacked up over a long period of time to form a not completely random thing. (Forgive me if my understanding is incomplete. Just kindly note the misunderstanding in a reply) But I see there being a problem if the process of evolution, which is guided by DNA, is essentially being undergurded by a complete and sudden random appearce of RNA.

Now again, I admit up front that my knowledge of science is amateur at best. So if you see flaws in my understanding consider them an honest mistake and not a flagrant intentional misunderstanding. Furthermore, if you feel that my correlation between DNA or RNA with evolution is not a worthy criticism of evolution please let me know.

I look forward to all replies and again please remind those who wish to reply that your comments please be gentle. I am stepping into the world of which I know very little, but want to learn more. So if on my first attempt of the riding the scientific bike, you feel that I've fallen down, just help me get back on my feet so I can try again. *Extends a gracious hand of welcome*

The implication that we should put Darwinism on trial overlooks the fact that Darwinism has always been on trial within the scientific community. -- From Finding Darwin's God by Kenneth R. Miller

Chaos and chance don't mean the absence of law and order, but rather the presence of order so complex that it lies beyond our abilities to grasp and describe it. -- From From Certainty to Uncertainty by F. David Peat

Incorrect. RNA is not a building block of DNA. RNA is nucleic acid polymer which is similar to DNA. In modern organisms it has multiple functions, for instance mRNA is used as an intermediate for transcription and translation, rRNA is used as a structural unit for the construction of ribosomal domains, and tRNA is used as a codon-domain binding assembler for amino acid sequencing.

(there are many more functions of RNA such as snRNA, snoRNA, cRNA, etc)

RNA is a molecule which is very similar to DNA, but has some obvious differences. Like DNA, it is made up of four bases bound onto sugar-phosphate backbones, but one of the four bases is slightly different. DNA is made up of A, C, T, and G. RNA is made up of A,C,G and U, which differs only in the prescence of a single extra hydrogen atom. RNA also has an oxidized form of the sugar ribose as the backbone chain, while DNA has a reduced version, deoxyribose, which is why one is called RNA and the other DNA. RNA also, unlike DNA, exists as a single helix, never a double helix.

Many scientists now believe that because it is isomerically less complex than DNA that it is the precursor of ancient life, which made the transition to DNA just under 4 billion years ago. How RNA-based life forms may have functioned is very difficult to assess as none exist as it seems that RNA has been totally outphased by DNA. But the RNA world hypothesis of abiogenesis holds a lot of weight because RNA is indeed an intermediate between simple bases and sugars, and the complexity of the DNA double helix.

but where did RNA come from?

Excellent question. Although it has quite an unstable base (U, which is why it was outphased by T), RNA's relative simplicity means that in terms of macromolecular covalescense it is capable of individual self-assembly.

is that RNA's origin is completely derived from chance.

Absolutely not, although simple compared to DNA, there is no way an isomeric structure like RNA could be a chance process. The process of proto-natural selection (Which precedes cellular life) is that stable conformations of macromolecules, whose size means an infinite number of possible conformations, would be a selective benefit to the propogation of these molecules. This, by the way, is how primordial protein domains originated, because biological polypeptides are all linked by the fact that they only adopt a single stable quaternery state, which is very unusual in nature. The answer lies in the fact that multiple-conformation domains are highly unstable and thusly are less likely to covalasce.

It is the same with RNA, really. In a dipolar solution like water, which has millions of organic molecules dissolved into it, polymerization is a readily occuring process (the dipole forces them together). The propogation of the polymeric structure depends on its conformational stability, which is where RNA undoubtably has a selective benefit.

This (biopolymeric assmeblage) too, is not chance. One falsely would assume that favorable formations of protein assemblage or RNA synthesis, whereby the natural quaternery state would arise is affixed the same probability as a useless denatured amino acid/base string. That is ridiculous, and has been debunked by the Miller-Urey experiment. Insofar as the nucleic acids and proteins of cellular mechanisms are primary life (ie they are capable of self-assembly), they undergo their own natural selection. This was demonstrated as far back as 1936 when Alexander Oparin showed that in an anoxic atmosphere, organic molecular structures of the basic primary state would combine to construct elaborate complex macromolecular giants which themselves were capable of reassembly. This is hardly unsuprising, protein strings undergo natural selection to confrom to the most stable state (all biological polypeptides have only one stable conformation).

The origin of the bases and small organic molecules underpinning these structures is a different matter, although they occur very readily in nature (while life has only 20 amino acids across the spectrum, there are over 100 in nature, and while it utilizes only 5 bases, there are over 300 on Earth). n 1961, Joan Oro, A spanish biochemist, cracked the adenine conjecture when he showed that the prebiotic nucleotide can assemble from hydrogen cyanide. Upon examination of comet traces, he concluded that comet fragments could have easily brought organic molecules to Earth. This in effect would merge Abiogenesis with panspermia except without the space aliens nonsense. His research paved the way for several more experiments, where the prebiotic synthesis of the other bases, thymine, guanine and cytosine, were demonstrated.

"Physical reality” isn’t some arbitrary demarcation. It is defined in terms of what we can systematically investigate, directly or not, by means of our senses. It is preposterous to assert that the process of systematic scientific reasoning arbitrarily excludes “non-physical explanations” because the very notion of “non-physical explanation” is contradictory.

Thank deludedgod for such a lengthy and thorough reply. I just have a few follow up questions for you.

The first would be concerning how you say that the formation of RNA is not derived from complete chance? Perhaps I missed a subtlety in your explanation, but I just didn't feel convinced that it is not. If you don't mind presenting perhaps a shorter explanation I may get the point you're trying to make.

The second thing, is mainly a remark, not a question. In my readings so far, the Miller-Urey experiment has been brought up many times. From what I've learned so far about it, I take a very skeptical position concerning this experiment. It is my understanding from what I've read that he most like got the molecular elements present in the experiment wrong compared to what the Earth was like pre-cellular. Also, it is doubtful whether or not we could ever replicate the pre-cellular Earth's atmosphere because ours is so highly saturated with oxygen. Furthermore, the experiments findings have not been able to be duplicated since the experiment's first testing. Is that true? How do scientist deal with that problem? I was just wondering if you could discuss your dealing with these criticisms of the experiment it self.

Lastly, I have heard of the panspermia theories deriving life's beginning from objects shooting in from outer space. This I feel only hurts the case that RNA (or what it's made out of) was not formed by chance. By positing the panspermia theory, it only shifts the problem to a different area, and begins a vicious regress.

I suppose in conclusion, I am not totally convinced that underlying the formation of RNA there was guided chance. To me, it seems like one theory attempting to patch the holes of another. Thank you again for your lengthy and highly explanatory reply. A lot of what you said have been covered by the great authors that I have read so far in my investigation. You are right on the mark. But if it wouldn't be too much trouble, please attempt a metaphorical round 2, based off what you said in this post, to try to explain how it wasn't a huge instance of chance involved in the formation of proteins and/or RNA.

*Forgive any improper phrasing. I hope I was able to make clear what my question entails. If you have any misgivings, just let me know and I will attempt to re-explain myself.

The implication that we should put Darwinism on trial overlooks the fact that Darwinism has always been on trial within the scientific community. -- From Finding Darwin's God by Kenneth R. Miller

Chaos and chance don't mean the absence of law and order, but rather the presence of order so complex that it lies beyond our abilities to grasp and describe it. -- From From Certainty to Uncertainty by F. David Peat

A way that I would think about is as so - lowest energy state conformers. As you know with the right combination of energy states, outside circumstances, etc. basic atoms combine. These new molecules then combine with other larger molecules, and so on. You might say - but isn't the RNA molecule so rare in that it was chance that it was formed and not some other molecule? The answer lies in the fact that molecules arrange themselves in the lowest possible energy state.

For proteins this is seen in tertiary and quaternary structure. Proteins fold into the lowest energy state in that they avoid steric hindrance and other energy problems [sterics refers to for example two negative charges being near each other ona molecule and thusly repelling each other]. This idea applies to the complex molecule RNA as well. Although the structure is different, we have the same principle in place. Thus it is not by chance that several molecules - i.e. a ribose, a phosphate, and a nitrogenous base came together in the way that they did. They bonded in such a way as to have the lowest possible energy (i.e. stable), avoid as much steric hindrance as possible, etc. Thus one could say that the progenitor molecules were destined to become something very like our RNA.

Biochemist & Law Student

"The day will come when the mystical generation of Jesus, by the Supreme Being as His father, in the womb of a virgin will be classed with the fable of the generation of Minerva in the brain of Jupiter." -Thomas Jefferson

A way that I would think about is as so - lowest energy state conformers. As you know with the right combination of energy states, outside circumstances, etc. basic atoms combine. These new molecules then combine with other larger molecules, and so on. You might say - but isn't the RNA molecule so rare in that it was chance that it was formed and not some other molecule? The answer lies in the fact that molecules arrange themselves in the lowest possible energy state.

For proteins this is seen in tertiary and quaternary structure. Proteins fold into the lowest energy state in that they avoid steric hindrance and other energy problems [sterics refers to for example two negative charges being near each other ona molecule and thusly repelling each other]. This idea applies to the complex molecule RNA as well. Although the structure is different, we have the same principle in place. Thus it is not by chance that several molecules - i.e. a ribose, a phosphate, and a nitrogenous base came together in the way that they did. They bonded in such a way as to have the lowest possible energy (i.e. stable), avoid as much steric hindrance as possible, etc. Thus one could say that the progenitor molecules were destined to become something very like our RNA.

Very interesting indeed my friend. I find what you said sensible enough and I just have a couple questions.

Have there been experiments outlining this "lowest energy state" combining event? And secondly, are there theories about why molecules act in a way so as to combine to form the "lowest energy state?"

Thanks for the reply thraxas.

The implication that we should put Darwinism on trial overlooks the fact that Darwinism has always been on trial within the scientific community. -- From Finding Darwin's God by Kenneth R. Miller

Chaos and chance don't mean the absence of law and order, but rather the presence of order so complex that it lies beyond our abilities to grasp and describe it. -- From From Certainty to Uncertainty by F. David Peat

There is something known as the Ramachandran plot in regards to proteins. It predicts the possible psi and phi angles of rotation on particular bonds in a protein. This addresses the possible conformations of the protein based on how much steric hindrance and too much energy there is.

The fact that molecules come together to form the lowest possible energy state is fundamental to chemistry, enzymology, and all the life sciences. It would be probably easier for me to draw you a graph - though I am not sure how I would put it up here. Pre cursor molecules will always start in a higher energy state. For example, say we have a deoxyribose and a phosphate [for examples sake]. These two molecules must get over an energy "hump" on their way to combining. This is called Ea or activation energy. This is the energy required by the deoxyribose and the phosphate to come together and bond. This barrier in energy is as the result of perhaps sterics, polar charges etc, which resist the bonding. Once this hump iis overcome the molecules come together and the energy state falls below that of the intial reagents.

There is a very important concept related to this. It is called Gibbs free energy. The equation goes delta G = delta H - T delta S. Where H is enthalpy and S is entropy. Thus for a reaction to go forward delta G must be negative (by this i mean, spontaneously). Enthalpy is heat essentially where entropy is disorder. This means the more disorder in the system, the more heat we need to add to make the reaction go. At some point the reaction will no longer be spontaneous if it is too disordered - i.e. you put one m olecule at the opposite side of the room from the other. But if you heat up the room they will start wiggling and perhaps moving towards each other if it is a gas [silly example]. If the reactino is spontaneous and thus delta G is negative, the subsequent product will have a lower energy than the original purely because it was spontaneous and it is more stable.

Biochemist & Law Student

"The day will come when the mystical generation of Jesus, by the Supreme Being as His father, in the womb of a virgin will be classed with the fable of the generation of Minerva in the brain of Jupiter." -Thomas Jefferson

There is something known as the Ramachandran plot in regards to proteins. It predicts the possible psi and phi angles of rotation on particular bonds in a protein. This addresses the possible conformations of the protein based on how much steric hindrance and too much energy there is.

The fact that molecules come together to form the lowest possible energy state is fundamental to chemistry, enzymology, and all the life sciences. It would be probably easier for me to draw you a graph - though I am not sure how I would put it up here. Pre cursor molecules will always start in a higher energy state. For example, say we have a deoxyribose and a phosphate [for examples sake]. These two molecules must get over an energy "hump" on their way to combining. This is called Ea or activation energy. This is the energy required by the deoxyribose and the phosphate to come together and bond. This barrier in energy is as the result of perhaps sterics, polar charges etc, which resist the bonding. Once this hump iis overcome the molecules come together and the energy state falls below that of the intial reagents.

There is a very important concept related to this. It is called Gibbs free energy. The equation goes delta G = delta H - T delta S. Where H is enthalpy and S is entropy. Thus for a reaction to go forward delta G must be negative (by this i mean, spontaneously). Enthalpy is heat essentially where entropy is disorder. This means the more disorder in the system, the more heat we need to add to make the reaction go. At some point the reaction will no longer be spontaneous if it is too disordered - i.e. you put one m olecule at the opposite side of the room from the other. But if you heat up the room they will start wiggling and perhaps moving towards each other if it is a gas [silly example]. If the reactino is spontaneous and thus delta G is negative, the subsequent product will have a lower energy than the original purely because it was spontaneous and it is more stable.

Hmm very interesting and very much out of my league. How do you think this explanation works in to the question at hand dealing with the origins of RNA?

The implication that we should put Darwinism on trial overlooks the fact that Darwinism has always been on trial within the scientific community. -- From Finding Darwin's God by Kenneth R. Miller

Chaos and chance don't mean the absence of law and order, but rather the presence of order so complex that it lies beyond our abilities to grasp and describe it. -- From From Certainty to Uncertainty by F. David Peat

I also found your explanation of the RNA world interesting, Deludedgod. I'd like to check and make sure I'm understanding it correctly. Is this right?

1. If you have a bunch of organic molecules floating in water, some of them clump together. The clumping is caused by natural properties of the water (bipolarity) and the molecules.

2. Some of the clumps are stable, and others are not. So this sets up a kind of selection pressure, since stable clumps ("conformations&quot will persist and become more numerous while the unstable ones will break apart, their pieces becoming vulnerable to getting "caught" by other stable clumps.

3. Because of the nature of its structure, RNA is more stable than other types of random clumps of organic molecules. So RNA clumps tend to stick around longer and become more numerous in a non-random, selection process. This part of the conjecture is supported by lab experiments.

Did I get it all?

"After Jesus was born, the Old Testament basically became a way for Bible publishers to keep their word count up." -Stephen Colbert

1. If you have a bunch of organic molecules floating in water, some of them clump together. The clumping is caused by natural properties of the water (bipolarity) and the molecules.

The polymerization is caused by the readily forming reactive bonds on the subunits. Due to the laws of thermodynamics, water cannot force this process to occur, but because it brings the necessary ingrediants together, it catalyzes the reaction.

2. Some of the clumps are stable, and others are not. So this sets up a kind of selection pressure, since stable clumps ("conformations&quot will persist and become more numerous while the unstable ones will break apart, their pieces becoming vulnerable to getting "caught" by other stable clumps.

"Physical reality” isn’t some arbitrary demarcation. It is defined in terms of what we can systematically investigate, directly or not, by means of our senses. It is preposterous to assert that the process of systematic scientific reasoning arbitrarily excludes “non-physical explanations” because the very notion of “non-physical explanation” is contradictory.

It is unlikely (I feel) that life formed just "sloshing about" in water.

There was a hypothesis about layers of sediment which went something like:

When you cover an uneven layer of stuff with another layer of stuff, the first layer tends to pass on its attributes poorly to the next layer. A sharp valley in the first layer becomes a rounded dip in the next, eg:

Dunno if that ascii art will come out right, but anyway... someone found that for some type of sediment this wasn't true - certain kinds of deformity were passed on rather well. These shapes evolved and persisted over "generations" (or rather, over layers of sediment) using a kind of natural selection.

They hypothesised that this sedimentary evolution might have turned into chemical evolution, and hence life.

Personally, I thought it was an awful argument but maybe they had more in support of their claim than I can remember.

But reason I brought it up was to point out that it's not just chemicals and creatures that are subject to natural selection. Any "population" of things is, where the following is true:
1) Most of the population is "tested" regularly (eg by a generation, a clump of molecules, a layer of sediment)
2) The results of one test has a bearing on the probability of its members (genes, molecules, sediment creases) surviving to the next test.

I think that's all it requires?

So, any situation where that happens could be the self-organising cradle of life.

So, any situation where that happens could be the self-organising cradle of life.

Where would that self-organizing tendency come from? Like what made the molecules that compose the building blocks of life combine.? Just being next to each other doesn't do it. I want to know how they are supposed to have come together to form something and how that tendency is explained.

The implication that we should put Darwinism on trial overlooks the fact that Darwinism has always been on trial within the scientific community. -- From Finding Darwin's God by Kenneth R. Miller

Chaos and chance don't mean the absence of law and order, but rather the presence of order so complex that it lies beyond our abilities to grasp and describe it. -- From From Certainty to Uncertainty by F. David Peat

Like I said, sloshing about in the ocean makes all that stuff unlikely. Goop in cracks in sediments is somewhat more likely: all the bits are at least near eachother. Other people have suggested that films of liquid on stuff might be where it happens. The oldest theory is a "soup" such that there are so many useful molecules around that they can't help but nag into eachother, but I find that a little hard to believe (maybe in a drying out pool, but not in any kind of stable environment). People have also posited hydrothermal vents on the sea floor as the cradle of life.

I can't answer your question, though, because there are too MANY possibilities.

http://en.wikipedia.org/wiki/Origin_of_life describes (in a couple of paragraphs each, so quite readable) genes-first, metabolism-first, the bubble idea, autocatalysis, the clay idea, deep-hot, the lipid idea, polyphosphates, and the ecopoesis model, along with a link to the mimivirus.

Hmm I thought I had explained this jread? Maybe I didn't do a very good job. ;] I feel like you are asking a more fundamental question of why anything chemically bonds. When we go down to the lowest level of two atoms bonding - lets say a sodium atom and a chlorine atom. In it's natural state is carries a +1 charge because it has 7 electrons out of a possible of 8 in its outer shell. The most basic explanation of bonding is that these atoms seek to create an octet ( electrons in their outer energy shell (aka orbitals). Then turning to chlorine, which carries a -1 charge. These two atoms comes together if they happen to be near each other in solution because their opposite charges attract and they bond ionically, sharing each other's electrons to give each other an octet and an overall neutral charge for NaCl.

This is the basic idea of at least ionic bonding. There are ionic or full negative and positive charges in complex molecules, however it is less common. You are more apt to see partial charges or dipoles resulting in covalent bonds. A dipole is a net partial charge on one or a group of atoms because one or more of them is more or less desirous of electrons (this is called electronegativity). Lets take H2O or water for example. Oxygen for certain reasons is more electronegative than hydrogen. Thus it pulls on the shared electrons between it and the two Hs in water more than the H pulls on those electrons. Therefore there is net negative partial charge on the O and a net positive partial charge on the Hs. This is very important for water in its ability to solvate. So essentially this dipole is not as strong usually as an ionic charge as in Na+ or Cl-.

So back to your basic question. Primordial soup is usually used to explain the initial formation of these complex molecules because it is unlikely that it could happen in any other environment besides in a liquid phase, particularly water. In the liquid phase, these molecules are able to bounce around due to various heat and the earth's radiation. Once they become close to each other, lets think in dipoles for a moment, a partial negative charge on the oxygen in a sugar is attracted to a hydrogen that is bonded to a carbon in a different complex molecule, the oxygen being so electron greedy feels those electrons and pulls and a bond forms.

This above is of course a tremendous over simplifcation of bondings. As sterics are involved, entropy, enthalpy, quantum orbitals and ab unch of other stuff. But I hope this helps - if you have anything else needing clarification let me know!

Biochemist & Law Student

"The day will come when the mystical generation of Jesus, by the Supreme Being as His father, in the womb of a virgin will be classed with the fable of the generation of Minerva in the brain of Jupiter." -Thomas Jefferson

I concur with the above poster. we are not talking about two molecules in a vast ocean. This soup must be a liquid that is small in quantity to allow a high heat (enthalpy) and a low disorder (entropy).

Biochemist & Law Student

"The day will come when the mystical generation of Jesus, by the Supreme Being as His father, in the womb of a virgin will be classed with the fable of the generation of Minerva in the brain of Jupiter." -Thomas Jefferson

Thank Dewimorgan and thraxas for your replies. They did make things a lot clearer for me. I just a couple questions that have to do with atoms and molecules.

I was wondering if something I've heard before is correct. I was told that scientists are unable to create water molecules. The example was that if you take the constituents of H20 before they've become bonded, like having just some H and some O, scientists can't make them combine to make water. Is this example correct? If the example is, then I have trouble seeing how molecules could've formed in the primordial soup. Is that scientists can't recreate the soup environment accurately? If scientists can't recreate it, then how do they know that their theory is the most likely scenario for the origin of life? I understand that the Miller-Urey experiment comes to mind, but there are a lot of criticisms of the experiments findings. I would love to hear about any other examples dealing the question about creating water and the "soup" theory.

Secondly, I have a little bit simpler question. When you spoke about atoms and their charges, I was wondering what creates or what is the cause of that attraction of electrons between atoms. I understand what happens (they want electrons) and seemingly why (because they are attracted)...But the why are they attracted? I understand that electrons, protons, and neutrons all have charges. But in pre-life earth, what caused this attraction? Was it magnetic ism created by the earth? Or can electrons, protons, and neutrons have attraction due to their charge when they are floating in space as residue from a comet?

I would appreciate any input very much. Thanks for all the replies thus far everyone.

The implication that we should put Darwinism on trial overlooks the fact that Darwinism has always been on trial within the scientific community. -- From Finding Darwin's God by Kenneth R. Miller

Chaos and chance don't mean the absence of law and order, but rather the presence of order so complex that it lies beyond our abilities to grasp and describe it. -- From From Certainty to Uncertainty by F. David Peat

Hoo boy, sliding well out of my comfort zone here: I never listened in chemistry.

Quote:

I was told that scientists are unable to create water molecules. The example was that if you take the constituents of H20 before they've become bonded, like having just some H and some O, scientists can't make them combine to make water.

Hee There's a really easy way to do it. This might help you guess:

thraxas wrote:

These two molecules must get over an energy "hump" on their way to combining. This is called Ea or activation energy. This is the energy required by the deoxyribose and the phosphate to come together and bond. This barrier in energy is as the result of perhaps sterics, polar charges etc, which resist the bonding. Once this hump iis overcome the molecules come together and the energy state falls below that of the intial reagents.

Another clue: hydrogen cars.

Final clue, then, if you haven't got it: hydrogen is flammable.

Burning it gives off energy, the hydrogen oxidises.... and water comes out.

You need to provide a little energy up front to get it over the wall, but it then gives off more energy than came out and the reaction is self-perpetuating, just like a gas stove.

But what if you just mix them together in a jar? Will water happen? No, I don't think so, because you haven't overcome "Ea": you need a bit of heat energy to activate the reaction that he talked about. A volcano, forest fire, the sun, lightning... some of the atoms might have enough energy to combine by themselves, but not enough to create a runaway reaction I don't think.

So, short answer: no, can't make water from two gasses in a jar no matter how much you shake them. Long answer: yes, easily, if you overcome Ea with a match.

That's why I like the "hydrothermal vents" idea - lots of spare energy kicking about to help any reactions along. Because of that, those things are just teeming with useful molecules.

Quote:

Or can electrons, protons, and neutrons have attraction due to their charge when they are floating in space as residue from a comet?

Sure they can! Nothing to do with life, or even earth: two oppositely charged particles attract eachother, wherever they are.

But why? How do photons make the particles attract? I have no clue, my knowledge ends there. For more information about why particles attract and stick together over various distances, try http://en.wikipedia.org/wiki/Fundamental_interaction - they know more than I do.

I am not sure who told you that water molecules cannot be created, but they are totally wrong. Water can be formed in many ways for example - putting together H2 and O2 - diatomic hydrogen and oxygen n the gaseous state. Add heat and you will get a reaction forming water molecules. Although both H2 and O2 are highly flammable so you might not want to try this at home lol. But you definitely get H2O very easily.

This example shows that often times heat is needed to get over that hump of activation energy, even in simple reactions. However this is not always the case, some atoms and molecules bond without heat or they use a catalyst to lower the activation energy such as an enzyme or an inorganic catalyst.

Attraction

Atoms are attracted to each other because of their charges, partial or full. The nucleus of atoms is composed of protons and neutrons. Protons contribute mass and positive charge, while neutrons only contribute mass (no charge). These positively charged protons pull on its own electrons to hold on to them, otherwise they would be released. This same idea works between atoms. The positive nucleus of say an oxygen pulls on the negatively charged electrons of a hydrogen. Because oxygen is more electronegative (this is a complicated concept that has a lot of physics behind it), it pulls harder on those electrons. The O and H bond with an unequal sharing of the electrons, with more of the charge going to the O because it "pulls" harder with its positively charged nucleus.

In terms of why they are attracted? This is asking why opposite charges attract. It has nothing to do with outside forces such as the earth's magnetic field. Electrons are fundamentally negatively charged while protons are fundamentally positve, always. If for example we were in a vacuum - a void of nothing - no gravity, no magnetism, no fields, no forces - nothing. And all we had were an oxygen and a hydrogen atom next to each other in this vacuum - this electron - proton attraction would still occur and they would still have these charges. The reason they attract each is because they create their own "mini" electromagnetic fields.

The reason that say an electron is negative is a larger question likely left up to quantum physicists. The interesting thingabout electrons is that they are both waves and particles. Very interesting indeed. In certain experiments they behave as if they were waves, scattering. However in others they act as discrete particles. This is called wave particle duality. Think in real life terms - a little circular crumb of cheese. This is the particle form. If it were an electron it would also be a wave, which sort of boggles our minds how something "solid" and "particulate" could also be a wave. In fact, ALL matter is both a wave and a particle. So indeed, YOU and me are both a particle and a wave. It is just that you appear to be particulate because you as a wave move very very slowly, that is a small period.

Another interesting thing about electrons is that you can not tell both the location and speed of an electron at the same time. That is, you can only calculate the speed or the position of an electron at a time. This is due to wave particle duality. ;p weird stuff huh. Oh and also you should think of electrons as clouds to represent the wave/particle nature - i know you are first taught to think of electrons as little orbiting balls - but they are more like clouds of negative energy.

;] haha anyway, bunch of theoretical stuff.

Biochemist & Law Student

"The day will come when the mystical generation of Jesus, by the Supreme Being as His father, in the womb of a virgin will be classed with the fable of the generation of Minerva in the brain of Jupiter." -Thomas Jefferson

But what if you just mix them together in a jar? Will water happen? No, I don't think so

Yep you are right. Water formation is an endothermic reaction that requires an input of energy (i.e. heat). It will never go forward without some catalyst. However this is not to be confused with very slow reactions. Some reactions are just slightly exothermic but are VERY VERY VERY slow. So if you put them together ina jar, they will react, but it might take 1000 years to reach equilibrium with the end product. This is the fundamnetal difference in that some people confuse reactions that will never go forward without heat and those that will but go slowly ("reaction order&quot - in either case it is impossible to tell witht he naked eye which is which.

Biochemist & Law Student

"The day will come when the mystical generation of Jesus, by the Supreme Being as His father, in the womb of a virgin will be classed with the fable of the generation of Minerva in the brain of Jupiter." -Thomas Jefferson

A very big thanks DewiMorgan and thraxas for your replies once again. I found that both of them were very helpful and removed some bad knowledge about the formation of water molecules.

I really appreciate the hydrogen and oxygen explanation. I understand how water is produced in the hydrogen car example; I remember hearing on the news how those engines are very environmentally friendly because their "exhaust" is water.

Furthermore, I found the explanation of attraction quite helpful as well. It's nice to know that the attraction of electrons to protons creates a mini magnetic field so they could still attract one another in space.

I suppose my only question would be to you both personally. Additionally, a question for anyone willing to it answer for me. Do you find that these theories are worthy of your trust? I noticed thraxas that at the end you said, "bunch of theoretical stuff" and I was wondering how confident you (or anyone else) feels in the theories that you explained to me. Personally, I find them worthy of confidence, but I just can't take that extra step and be confident enough in them to have been one of the driving forces behind the origin of life.

So if you would please indulge me with a little bit of personal sharing as to your feelings concerning your confidence in scientific theories, I would greatly appreciate the read.

Thanks again for your replies guys, my background in Bio 100 and Phys 151 (Intro) thankfully let me understand what you were saying enough to comprehend the overall meaning. Kudos!

The implication that we should put Darwinism on trial overlooks the fact that Darwinism has always been on trial within the scientific community. -- From Finding Darwin's God by Kenneth R. Miller

Chaos and chance don't mean the absence of law and order, but rather the presence of order so complex that it lies beyond our abilities to grasp and describe it. -- From From Certainty to Uncertainty by F. David Peat

I have great personal confidence in these theories. I have studied them greatly and there is a vast amount of experimental data that supports them. And when I said "theoretical" stuff I was more referring to complicated scientific ideas - not in a sense that they were unproven nor not very welll proven. As most of the ideas I have mentioned to you have been known for a very long time, the latest at the turn of the last century.

Why can't you take them to heart as the origin of life? No one can know for sure what happened at the dawn of our planet. But we do know that life arrived, as we are here and all other life. We have abundant knowledge about the basic chemicals and molecules that life requires. We know how they behave in the lab and nature of today. It is certainly a good hypothesis that these same interactions occurred at the beginning of our earth. This early earth was very active geologically - specifically volcanically. Let's imagine perhaps a scenario --

A lifeless earth, not even archaen bacteria (ancient bacteria that is still alive today). Over many years strong winds, rain, and volcanic debris has weathered the grand mountains of our planet. This eroded debris from a mountain slowly collects to form a loose sediment (i.e. dirt) at the base of the mountain - a mountian that has a volcanic vent. This sediment grows quickly because previous outpours from the volcano left chunks of solid basaltic lava which had hardened and is easily broken down by rain. This this new loose sediment or dirt has formed, it begins to rain again, as paleoclimatologists have evidence for a violently climatic earth. The rain comes down in torrents soaking the loose sediment and the surrounding rock. A small pool has formed from the curvature of the surrounding rock at teh base of the mountain, this is a pool that is thick and soupy as it is filled with the loose debris (now we would call it mud!). ..... continued

As the pool formed from the rain, the loose sediment, as it became "mud" like, began to be solvated - that is broken down by the water. The pool is murky and brown. Due to the ability of water to solvate most anything, the dirt is broken apart into its smallest pieces - small carbon molecule chains, nitrogens attached to carbons, phosphates, and other inorganic elements. In addition we have more hydrgon and oxygen in the form of water. Suddenly an earthquake occurs, and the pool is destroyed. thousands of years pass and a few of these pools recurr.

The pools being right above volcanic vents (the earth was extremely actively volcanically then), the pools are heated greatly, some to boiling. This heat drives the molecules to fly about the pools as if racing about, slamming into each other and bonding when appropriate [as in my post about bonding and when and how it works]. A few smaller molecules form more complex molecules. These molecules arrange themselves into the lowest energy conformers, as if they donot, they likely will break apart due too much energy - thus we have the most stable conformers or isomers of our beginning complex molecules. This process builds until we have RNA. RNA eventually associates with lipids that had formed from long carbon chains and phosphates. These lipids formed in a sphere around the RNA due to entropy and the property of the lipids on one side to be hydrophobic (water hating) and the other side water loving or hydrophilic. Thus the phosphate part of the lipid is on the outisde,and the carbon chain on the inside. Alas some of the water is trapped in the new container annd it also contains a grouping of the molecules that were in the pool along with the RNA molecule. More lipids bunch into the membrane and rearrange so that the carbon chains are free from that hated water, so we get a lipid bilayer, with phosphates pointing both to the outside and to the watery inside.

And tada we have an progenitor prokaryotic archaen bacteria.

The answer of science is so beautiful - and this is only one possible route. In my opinion not only do we have tremendous evidence for all of this from our present knowledge, but it is also a more simple and elegant explanation than inserting the extremely complicated idea of a god. You don't give "nature" where credit is due. ;]

Biochemist & Law Student

"The day will come when the mystical generation of Jesus, by the Supreme Being as His father, in the womb of a virgin will be classed with the fable of the generation of Minerva in the brain of Jupiter." -Thomas Jefferson

For me it all comes down to the hypothesis factor surrounding the origins of life as the reason why (right now) I can't accept them with confidence. I suppose since I have always been accustomed to the idea that God created everything, going from a sure explanation to a hypothetical one is difficult. I understand that those who don't believe in God will say that believing that God created everything is way more hypothetical than believing in the scientific explanation. I grant that it does seem more hypothetical to believe in God as the creator, but none the less, it still difficult to take a leap of faith that I am not accustomed to, nor know anything about. This is why I want to learn about it, so I can know something about that which I am having trouble accepting.

Some of the problems that I am having with accepting the scientific explanation which you have so clearly layed out for me, is the idea of congruence. I got this term from the book I'm reading where it basically explains the term 'congruence' as searching for explanations to things in the past based on how things work today. For example, the way metabolism works today is how they search for answers how metabolism worked yesterday (Billions of years ago). This congruence presumption is very problematic for me. I am having great trouble accepting that the earth a long long time ago, is how we think it was, when we really don't know how it was. (sorry for the confusing sentence). It seems to me, that there is nothing about today, that can conclusively explain what happened yesterday. Now I understand that there is evidence to back up the theories proceeding from the idea of congruence. But, I am just having trouble accepting that the evidence is actually able to explain anything about how the earth was so long ago. It seems that so much of the Earth's surface has changed since the prebiotic period, that how can evidence lasting today having anything supportive to say about how it was billions of years ago.

One answer Mr. Duve gave, had to do with the oldest bacteria known using sulfur in some of their chemical processes. And that sulfur is in two of the (bases?) for a protein(?). He draws the conclusion from the lasting remnants of sulfur in this still lasting bacteria and protein(?) that life in prebiotic times was how they think it was (Containing lots of sulfur from volcanoes).

All and all, those are just some of the reasons why I have withholdings about accepting the scientific explanations for how life on Earth was created. If you could give me any further advice on the reliability of using a congruence strategy of investigation into the origin of life, I would greatly appreciate it.

Thanks again for another great reply and I hope that I am not being a bother to you by asking, seemingly, the same question over and over. I want you to know that I have a genuine desire to learn about what I am unwilling to accept thus far.

[Note: The (?) were after terms that I thought I might've mixed up or misnamed. If there are any others that I may have confused/misnamed I apologize.]

The implication that we should put Darwinism on trial overlooks the fact that Darwinism has always been on trial within the scientific community. -- From Finding Darwin's God by Kenneth R. Miller

Chaos and chance don't mean the absence of law and order, but rather the presence of order so complex that it lies beyond our abilities to grasp and describe it. -- From From Certainty to Uncertainty by F. David Peat

Hello again. I found a very interesting article about a repeat of the Miller experiment that had repeated failure. It was re-attempted this year with success. The re-attempts of the experiment had previously failed because the spontaneous chemical generation of amino acids (protein precursors) were being destroyed by nitrite by products. Scientists could not understand this until they realized that the old earth was heavy with iron and carbonate minerals which neutralize the nitrite. When this new experiment was performed, the same result was obtained as the old Miller experiment - stable amino acids sponatenously formed. This experiment was performed by Jeffrey Bada at the Scripps Institute of Oceanography if you want to peruse/look it up.

In terms of your "congruence" ideas. First off - we have massive amounts of evidence that tells us about how our earth was billions of years ago. Let's just look at one area of study called Paleoclimatology which studies the climate of our old earth:

Inside of glaciers and ice caps scientists have found pollen allowing them to estimate the amount of ancient plant growth for a given year, certain layers contain ash from volcanic eruptions. Air bubbles become trapped in the snow and is compressed into the hard ice sheets. These air bubbles are used as direct measurement of what our air was like all this time ago. Evaporation and thus glacier levels of various hydrogen/oxygen isotopes also clue us in on ocean temperatures.

Sedimentary rock is studied also for climate. The changes in the climate of the earth is quite visible from the beginning in this rock.

Our earliest rock dates to 4 billion years old which has biogenic carbon. We have fossils of stromatolites from. 3.7 billion year old rock. Descendents of these stromatolites are still living today in a few places on earth.

Thus we have a ton of data from old rock, glaciers and fossils to support how the climate was long ago. Through the geologic record we can see the various layers going back billions of years - what the rock was made of, how old it is, what minerals and chemicals it has, if there were organisms, the levels of isotopes to tell of the climate/temperature etc. The geologic record is extremely reliable and telling as we can see the distinct band of rock - its amazing to look at and think - this rock is billions of years old and here it still is. It is not as if this rock has disappeared, but it still exists today and is studied.

I urge you to think about these ideas and the tremendous about of evidence that back them up. I understand the misgivings based upon the position you have been raised in. And you also say "leap in faith". In fact to believe in these ideas, no faith is needed at all! Faith is belief without evidence, and these theories have great amounts of evidence to support them. You only need to think about them and view them to see their validity. Think about it this way - you go from believing a hypothesis with absolutely zero proof (god) to something that has a lot of proof (these scientific theories).

Biochemist & Law Student

"The day will come when the mystical generation of Jesus, by the Supreme Being as His father, in the womb of a virgin will be classed with the fable of the generation of Minerva in the brain of Jupiter." -Thomas Jefferson

Firstly (even though it was the last point in your message, it's important enough to respond to first): you are not being a bother! You (and this thread) are one of the coolest things here, and the reason I keep coming back. Questions like yours make the forum seem worthwhile, despite all the threads of people shouting at eachother with their fingers in their ears.

To me (others will disagree), believing in God is not a problem so long as you follow up every "God did it" with the question "so, how did He do it?"

The danger with a God of the Gaps is that it can make people stop looking for answers. It happened to Newton. He couldn't do the math to get the planetary movements to work together using his theory of gravitation, so he put his hands in the air and said that such a complex system could only be controlled by God. People came along later and invented calculus, and did the math, and found that it matched up very well with Newton's laws of gravitation (and even better with Einstein's tweaks).

Every mechanism He has used, from gravity, to weather, to radiation and electricity and lightning.... has always been explainable. Sure, it's possible that God decides where and when the lightning will strike, and what shape each cloud will be at each point in time... but now we know how he makes the lightning strike, the water flow in the streams and the clouds form and things fall from the sky and creatures change over time and wood burn and the planets and stars move in their orbits and the sun glow...

So, if He forms universes and life... how does He do it?

Given what we've seen so far, they'll most likely be something beautifully elegant, and which we can understand, just like all the others.

Why are those two so hard compared to the others? Because they only happened once! We have to guess back in time.

Which wittering brings us to the next bit.

The only thing I can give to support our belief in the current idea of the past is that we have a fair number of records stretching back in time to the beginning of life, of the world, and of the universe. These independently support eachother.

As an example, I made a list of stuff used in dating stuff on earth: other stuff is used in dating non-earth stuff, but there is considerable overlap, and cosmological stuff ties in with earth-stuff.

To test any hypothesis, we make predictions and see if they turn out true. Like "These monkeys and apes all have the gene to make an antibody to defeat this virus, which from the differences between them seems to have been a big problem about X million years ago: let's see if these isolated madagascan monkeys have the same gene: they shouldn't, because they were isolated at the time the virus was around, so shouldn't have needed to develop the antibody, hey they don't, waytago us!"

Not a great example, but you get the idea.

[Edit: thraxas: You are seriously making me reconsider my decision not to make a list of awesome atheists as well as theists I must grumble about your news about the Miller experiment, however. Not because I disagree, but because I am now going to be procrastinating for hours reading up on it. You evil git.]

For me it all comes down to the hypothesis factor surrounding the origins of life as the reason why (right now) I can't accept them with confidence. I suppose since I have always been accustomed to the idea that God created everything, going from a sure explanation to a hypothetical one is difficult.

OK, let's deal with this. You are quite correct, each brand of theism claims to have a profound, and convieniently simple and succinct explaination for how we got here and why things are as they are. Your explaination is not the same as the Muslim explaination or the Greek explaination or the Native American explaination - yet at their core, all of these explanations are seeminingly similar and equally valid. They all rely on tradition and revelation - two of the worst reasons to believe anything.

You are quite right, science WON'T provide you with a nice neat answer that fits in your pocket. That simply is not how science works. Science is provisional, it changes as we learn more, it makes no dogmatic claims, has no master, obeys no creeds.

A scientist is COMFORTABLE saying "I do not know" - a religion never is.

As a scientist, I'm comfortable, given my understanding of the universe, that no Creator is required. That could change given new evidence, though given the trends of things in the bilological and cosmological community, I doubt such will happen.

Still, my take on the universe is an inductive one, based upon the best evidence I have available. I cannot claim certainty, for science is NEVER certain.

Black and White simple explanations are for children. Adults are comfortable with a degree of uncertainty and have the ability to gauge probabilities.

We are all well aware of the law of gravitation, but there does remain the possibility that apples will rise rather than fall from trees tomorrow. Inductive reasoning and observation allow us to gauge how concerned we ought to be chasing down the fruit on our cereal tommorrow.

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I understand that those who don't believe in God will say that believing that God created everything is way more hypothetical than believing in the scientific explanation. I grant that it does seem more hypothetical to believe in God as the creator, but none the less, it still difficult to take a leap of faith that I am not accustomed to, nor know anything about. This is why I want to learn about it, so I can know something about that which I am having trouble accepting.

I DO understand where you are coming from. It is tought to go from "certain" answers to provisional ones. The first step comes in assessing how "certain" those answer you used to have really were. Why did you believe them? Why did you trust them? What evidence did you have? Do you have valid, logical, evidence based reasons for believing what you believe?

It really is as simple as that.

Scientifically speaking, you have to be willing to trade unfounded dogma for what Sagan described as "happy uncertainty" and "provisional truth". You have to be willing to base belief on the best available evidence, no matter where it leads you - that is the closest to truth we can get.

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Some of the problems that I am having with accepting the scientific explanation which you have so clearly layed out for me, is the idea of congruence. I got this term from the book I'm reading where it basically explains the term 'congruence' as searching for explanations to things in the past based on how things work today. For example, the way metabolism works today is how they search for answers how metabolism worked yesterday (Billions of years ago). This congruence presumption is very problematic for me. I am having great trouble accepting that the earth a long long time ago, is how we think it was, when we really don't know how it was. (sorry for the confusing sentence). It seems to me, that there is nothing about today, that can conclusively explain what happened yesterday.

To the contrary, there is an enormous amout of evidence that allows us to piece together how things were yesterday. You chose digestive systems as an example. We can start by looking at the flora and fauna that were around during the time of the individual in question via the fossil record. This is what the animal COULD eat. Now lets look at its chompers. We can tell from the animals teeth what sort of diet it had - partly from comparison to existing organisms but also by common sense; big canines indicate a predator, big grinding molars would indicate a grass grinder. Now we DO work backward in evolutionary tales - they are like history books. We look at the fossil record (not just of the species in question, but the plants and animals it lived with), we look at morphology (the traits of a good predator tend not to change much over time - big tooth and claw, fast and powerful), we look at genetics - what genotypic and phenotypic traits to species we believe are descendent have? How would we expect them to change over the eons?

To say we can know nothing about the past by observing the present (and really as it happens snap shots of the past) seems a bit of a stretch to me.

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Now I understand that there is evidence to back up the theories proceeding from the idea of congruence. But, I am just having trouble accepting that the evidence is actually able to explain anything about how the earth was so long ago. It seems that so much of the Earth's surface has changed since the prebiotic period, that how can evidence lasting today having anything supportive to say about how it was billions of years ago.

A very simple example would be that all life on earth shares the same biological alphabet. Be it in smokers on the ocean floor or humans, all life on earth derives energy from the same basic bilogical interactions. All life on earth uses the same set of amino acids. All life on earth has their protiens and RNA and DNA twisted to the same chirality. The best and most scientific explaination for this is that all life on earth shares a common ancestor. This explanation is supported by the fossil record, geologic column, genetic studies, simple logic, Occam's Razor, and evolutionary biology.

That is what science tells us, given the evidence at hand.

Or, if you prefer certainty, you can just throw your hands in the air and say, "God did it".

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One answer Mr. Duve gave, had to do with the oldest bacteria known using sulfur in some of their chemical processes. And that sulfur is in two of the (bases?) for a protein(?). He draws the conclusion from the lasting remnants of sulfur in this still lasting bacteria and protein(?) that life in prebiotic times was how they think it was (Containing lots of sulfur from volcanoes).

I don't know how this is an objection. There are PLENTY of bacteria that are still around today that derive energy from sulfur compounds. You need only look at the smokers on the ocean floor I just mentioned.

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All and all, those are just some of the reasons why I have withholdings about accepting the scientific explanations for how life on Earth was created. If you could give me any further advice on the reliability of using a congruence strategy of investigation into the origin of life, I would greatly appreciate it.

It seems to me, what you REALLY want is a certain answer. You won't get one here. You'll get an HONEST answer, based upon evidence. If you want certainty, you know where to go and what it is worth.

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Thanks again for another great reply and I hope that I am not being a bother to you by asking, seemingly, the same question over and over. I want you to know that I have a genuine desire to learn about what I am unwilling to accept thus far.

I do appreciate what appears to be a genuine interest in understanding what others believe and why. I applaude that. I'm sure it will effect in in some way, perhaps falling short of chaning your mind, but certainly giving you a better idea of how the other half thinks.

I am against religion because it teaches us to be satisfied with not understanding the world. - Richard Dawkins

Hmm very interesting indeed about the glaciers and geological records. I followed and understood everything you said in your reply. I appreciate your time and effort very much. I just have a couple questions and one comment.

In regards to the leap of faith I mentioned. I understand that science provides evidence, but I would still consider abandoning my faith a leap of faith. Perhaps more analogous to what it is that I am leaving, not so much about what I am going to. Or in other words, In my imagination it takes a leap of faith to leave faith. At this point, I wouldn't worry about me losing faith in God. I honestly have a near identical view of how DewiMorgan explained a possible God believer scenario desire to understand science and how the world works. So as that as my ultimate aim, losing faith would be a mere byproduct not an ultimate goal or ending.

I hope deeply that this doesn't discourage your willingness to answer my questions. I have a relentless fervor to discover the scientific theories explaining the origin of life. Now that you have laid out quite well the theories, and answers to support those theories, I would like to shift gears and ask perhaps tedious simple questions.

First, how reliable is the dating system that scientists use to date rocks, bones, etc. I suppose it's carbon dating. Have they done any blind experiments where they have 3 different types of bones, 2 where they know exactly how old they are and 1 they have no clue? Presumably then basing their dating system's reliability on the successful dating of the known examples to infer the age of the unknown example? Have any such experiments occurred? What do you feel is the best piece of support for out current dating mechanism/process?

Secondly, is it possible that rocks/bones/organisms could change over the time when they've been frozen? Like could prolonged exposure to icy surroundings cause the aging process to seemingly speed up or slow down? Or could the cell/organism continue to grow even when it is frozen, resulting in a inaccurate preservation of how the cell/organism originally was? Additionally, could exposure to heat over many years affect the remaining part of the cell that would ultimately render is quite different from how it originally was?

So these questions I have now could basically encompass the more general question of:

How reliable is out dating system? Is there reason to doubt it? If so, what are those reasons to doubt it? If not, then what are the reasons to accept it?

Any replies would be much obliged again thraxas and dewimorgan. I very much appreciate you both sticking with me for the long haul. Cheers.

Lastly, thanks for the Miller experiment update. I will hold the experiment in higher esteem knowing that it has been able to be reproduced.

The implication that we should put Darwinism on trial overlooks the fact that Darwinism has always been on trial within the scientific community. -- From Finding Darwin's God by Kenneth R. Miller

Chaos and chance don't mean the absence of law and order, but rather the presence of order so complex that it lies beyond our abilities to grasp and describe it. -- From From Certainty to Uncertainty by F. David Peat

I do appreciate what appears to be a genuine interest in understanding what others believe and why. I applaude that. I'm sure it will effect in in some way, perhaps falling short of chaning your mind, but certainly giving you a better idea of how the other half thinks.

Thank you very much for your reply Y.N.F. I just want to give you a bit of clarification about what I meant by some of the things I said and give you a glimpse into what my true motives are behind asking these questions.

First, the example about the sulfur and bacteria, wasn't an objection, I was just wondering if this can/does tell us about the state of the prebiotic Earth. I find the example very intriguing and only mentioned as a reference to guide my questioning concerning theories about the condition of the prebiotic Earth through using ancient bacteria in this instance.

Secondly, I am not looking for certainty in the answers that science can provide for me. I find that certainty is something that can never possibly be attained. Let's just say, I really like what David Hume has to say on the subject. He's my favorite philosopher to study.

Ok, so those were the clarifications of my comments. Now for the clarifications of my motives. My first motive is to take a skeptical position concerning current scientific theory and ask the questions that I can come up with to test the theory's ability to answer. My second motive, is to gain a genuine understanding of the thing which my beliefs ultimately force me to reject as the origin of life. I am not asking these questions to be an annoyance. I have a genuine desire to learn and understand. And just to ease your heart, I've never been a believer to pretend that I have the answers to all of life's questions. The background in philosophy that supports my character forbids me to even acknowledge that I know something definite about what God really is. The possibilities are truly endless when you try to "nail down" a certain definition of God's nature.

Hopefully that bit of clarification will help you understand why my presence has been in this forum for the past few days. It is not to poke and prod the scientific community all the while I plug my ears and stomp my feet. Rather, I am here to truly learn about that which I know nothing about, and that which my belief requires me to reject as the explanation for the origin of life. I believe that if I am going to reject something, I should atleast know the basics of what it is about. And it just so happens that the basics of science is not enough for me at this point in my life. I want to learn as much as I can in my personal study. I have chosen this place as an outlet for further searching outside of the pages of the books which I have lined up for my pleasure reading during the summer. Good evening to you and welcome to my mixed up mind.

The implication that we should put Darwinism on trial overlooks the fact that Darwinism has always been on trial within the scientific community. -- From Finding Darwin's God by Kenneth R. Miller

Chaos and chance don't mean the absence of law and order, but rather the presence of order so complex that it lies beyond our abilities to grasp and describe it. -- From From Certainty to Uncertainty by F. David Peat

First, how reliable is the dating system that scientists use to date rocks, bones, etc. I suppose it's carbon dating. Have they done any blind experiments where they have 3 different types of bones, 2 where they know exactly how old they are and 1 they have no clue? Presumably then basing their dating system's reliability on the successful dating of the known examples to infer the age of the unknown example? Have any such experiments occurred? What do you feel is the best piece of support for out current dating mechanism/process?

Reliability is an interesting question. Most all of the dating techniques are reliable in the sense that they work for a proper date range. For example radio carbon dating (C-14) is only reliable for around 40,000 years and is usually used in human archaeology. This is because radio carbon dating is used based on the half life (how quickly a radioactive isotope decays) of certain molecules in the sample. Just a few of the lists of many, many types of dating include argon-argon, helium-helium, neon-neon, potassium -argon, various types of uranium.. and the list goes on. Most of these are able to date rocks and organisms into the billions of years. Typically the dating is done on the ROCK not the sample unless you are speaking about relatively new things (i.e 40,000 years).

The dating is done on the rock because often the isotope we are looking for to be used in the dating is inorganic and is not found in organisms (like uranium!). It goes that if an organism is deposited ina particular sediment layer, it must be of the same age as the rock (makes sense right?). With these older dating methods we can't really do the experiment of comparing it to a known sample like we can do in radio carbon dating - however once we figure the age of a rock with the technique we can use this original sample as a model.. however..

Lets do an example in Uranium - lead dating. It is one of the techniques that can date very old rock. It ranges from 1 million to 4.5 billion years. It is precise to within 0.1-1 percent. The techinque relies on measuring hte decay of two isotopes of uranium and lead. Uranium has a 4.76 billion year half life and lead has a 740 millino half life. The accuracy of the technique is due to the two indepedent chronometers of uranium and lead. Thus scientists can use both isotopes to determine how much of the isotope is left and compare it to the half life to determine age.

Thus dating techinques are extremely reliable in all contexts. Furthermore, different techniques (using different isotopes) have been used to cross check dates and they have always concurred. In the totality of science, radiometric dating is one of the most assured things to be truthful, based on the number of independent techniques and the prolific use. These techniques are also supported by other techniques such as glacier observation, geologic deposition, and dendrochronology.

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Secondly, is it possible that rocks/bones/organisms could change over the time when they've been frozen? Like could prolonged exposure to icy surroundings cause the aging process to seemingly speed up or slow down? Or could the cell/organism continue to grow even when it is frozen, resulting in a inaccurate preservation of how the cell/organism originally was? Additionally, could exposure to heat over many years affect the remaining part of the cell that would ultimately render is quite different from how it originally was?

Well, we would never find anything of interest in a glacier or frozen. What I mean is that sure, we can find a man from the ice age as you probably have seen on television - or a wooly mammoth - but we are talking about ancient (billions of years) stuff. These organisms are traditionally never found in ice but only in sedimentary rock as fossils. However, there was a recent thing found somewhere in the arctic - archaen bacteria that were buried under the top layer of arctic tundra were still living and were determined to be over 2 billion years old! It was amazing to hear about. I have to find the article about it. They were found in spore states which is essentialy suspended animation. When they were put into flasks with feeding media, they came out and started eating and such.

Onto finding fossils and such. As I said they are almost always found in sedimentary rock. You ask whether they can change over time. Yes, they do the process is called taphonomy. Fossils are first permineralized which means that minerals creep in and grow in open spaces such as cavities in bone. The fossils are usually also compressed and such. So dating can be done on the minerals that grow into the organism due to permineralization. It must be noted that the MAJORITY of organisms that die are actually destroyed. That is - for various reasons the fossils do not survive the process or are never discovered. However, we do have many many fossils and most are in excellent condition.

Even if we found something in ice it would not be changed from whence it was deposited. Even bacteria that are able to survive very long in such a state go into a spore and are essentially in suspended animation. Everything else that might be stuck in ice or rock is definitely dead ! ;D Therefore only outside processes work on it - no more internal growing of course. You mention cells quite a bit. The only time we can really get old cells is through the bacteria I mentioned. Everything else has been permineralized and the poor organism has been essentially turned into a rock. .. however..

Hardened amber can trap ancient insects and one can actually extract the cells from them. You may have seen this in Jurassic park - although you cant really do what they did lol. But we can get cells from at least 65 million years old that way. However we do not really need ancient cells to analyze the date at all (we use rocks to date) and we have living todya ancient bacteria which tells us the most early type of cell.

Biochemist & Law Student

"The day will come when the mystical generation of Jesus, by the Supreme Being as His father, in the womb of a virgin will be classed with the fable of the generation of Minerva in the brain of Jupiter." -Thomas Jefferson

I honestly have a near identical view of how DewiMorgan explained a possible God believer scenario desire to understand science and how the world works.

Excellent. I was describing the mindset I went through as a teen: I felt it to be eminently rational. The only thing that has changed over the years is that now know far less than I did then, but am confident that all the gaps in my knowledge are at least partially filled by what others know. Which leaves me with no gaps to fit a god into

Or, put another way: other people's knowledge is my personal god of the gaps.

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First, how reliable is the dating system that scientists use to date rocks, bones, etc.

In my list above, where you see a percentage, that's how accurate it is: I am afraid I was unable to find percentages for all of them, but Google may help. Some are nice and accurate, better than 1% (Uranium-lead can be as accurate as 01% in ideal conditions): others are pretty sloppy, 10% or so. Yet others are "relative". All they tell you is "X is older than Y". So, with superposition, you can say "well, this was laid down ontop of that, so this must be younger than that".

The best dating methods, I feel, are those that let us pin down the exact year: dendrochronologies, sediment records, ice cores. They have an accuracy of +/-6 months either way, as far back as they go. assuming they counted the layers correctly, at least

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I suppose it's carbon dating.

That, and the 37 other methods I listed, and doubtless plenty more I don't know about

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Have they done any blind experiments where they have 3 different types of bones, 2 where they know exactly how old they are and 1 they have no clue?

Certainly not! Well, perhaps in first year archaeology courses in university, where they just wanted to prove the point to students and don't want them to do too much work.

But to properly calibrate any dating method, you need to compare it to many many samples, which have been reliably dated with multiple other dating methods. A single unknown just wouldn't do.

Most significant archaeological finds are dated using at least two methods, as a cross-check. If there's any discrepancy, then they test with more methods, and find the reason for the discrepancy. Once a discrepancy is found, this can result in revising or re-testing dates of other finds that were dated with just a single method, but nowadays such revisions are very few and far between.

For radioactive methods, you're also testing against the math of radioactive decay. Your dating hypothesis will say that there was a "reset event" - when carbon was last burned, when a rock last reached 650 degrees C, when it last had a working metabolism, when it was last exposed to air or sunlight, etc.

You are measuring the time since that reset event, which is not necessarily the time it was buried.

Knowing the halflives of the two things X and Y that you are measuring, you can say that it will start out with a certain amount of X and Y, each one decaying at an absolutely constant (percentage) rate. If your two things decay at different rates, then simply by knowing the initial ratio at the reset event, and testing to find the current ratio, you can work out the date until the reset event.

Uncertainty comes from two inaccuracies.

The first is inaccuracy in knowing the half-life if you only know an element's half-life to 3 significant figures, you'll only get a date accurate to 3sf at best.

The second is not knowing whether you can guarantee that in the past, the isotopes were in the same ratio in the environment as today. This is the reason that calibrating the dating, ideally against multiple known yearly-cycle methods (ice cores, wood rings, lake sediments, stalactites, etc), is critical.

C14 dating is a good example. We know there is a lot more C14 in the air since we began atmospheric nuclear testing, so if we extrapolate from today's ratios, everything becomes horribly inaccurate around the 1940s.

We established this by taking the dendrochronology calendar and testing samples of wood of known ages (and even specific rings of wood within those samples) and testing their C14/C12 ratio.

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What do you feel is the best piece of support for out current dating mechanism/process?

The fact that whenever multiple dating methods are used on a sample, they give the same answer. When they don't, it's an exciting and unusual event and leads to increases in dating accuracy as they work out why not.

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Secondly, is it possible that rocks/bones/organisms could change over the time when they've been frozen?

Easiest answer here is "I dunno" I don't know if temperature affects decay rates. It may do. If it does, I am confident that it is taken into account in establishing the accuracy of the dating method. Personally I suspect it does not, for the simple reason that half-lives are never specified with a temperature component - just a time. It's "5740 years" not "5740 years at 50 degrees".

Reset events are generally chosen so that they can't happen a second time without noticing them. If the rock was melted again, or the wood was burned again, or the animal came alive again, there should hopefully be some sign that would tip you off. So, there *should* be nothing that would reset or upset the ratios. But, just to be sure, they use at least two accuratedating methods anyway, plus the usual sanity checks like "well, this strata we're digging in is between that one and the other one, so I'd be surprised if the date wasn't somewhere between the two."

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Or could the cell/organism continue to grow even when it is frozen, resulting in a inaccurate preservation of how the cell/organism originally was?

More likely is outside contamination. If the critter died, but some microcritters got into its fossil and set up home there, they could bugger up the C14/C12 ratio, by being alive at the wrong time and contaminating the sample with their modern ratios.

This would make the sample seem younger than it should, not older, though, so wouldn't support the young-earthers.

People are always on the lookout for organisms or processes that might selectively eat or erode one isotope without taking away the other - that would bollix up the dating.

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Additionally, could exposure to heat over many years affect the remaining part of the cell that would ultimately render is quite different from how it originally was?

Well, yeah, burning it will do that. But it's the kind of thing you notice. Lava has some unique problems, too.

Soft-tissue tends to dessicate in prolonged dryness: mummification. All the water evaporates from the cells, their cell walls rupture and collapse. But the isotopes don't tend to change their ratios due to the lack of water.

In a wet heat, though, soft tissue doesn't tend to survive at all. But the bones remain with the same isotope ratios.

Just to add to thraxas' point about amber: as far as I know, no DNA has been recovered from amber, though I may be wrong.

Yes there has been no DNA successfully taken from amber, though they have taken cellular tissue. All the items that dewi points to in regards to your questions about samples changing only relate to relatively recent samples i.e. 40,000 or so years - the range of radio carbon dating. As I mentioned, only relatively recent samples have been found in ice, unless you are talking about older pollen, but I was thinking more of ancient animals and complex organisms.

Decay rate or half life of isotopes is independent of temperature in any dating method. The exponential equation goes N(t) = N0 e^-(lambda)t. Where t = time in years (usually). N(t) is the amount after t years. lambda is the half life or decay constant.

But either way, I figured that jread was getting at very old samples/fossils, not relatively recent human archaelogical or mammal samples. All the effects that you are concerned about in your question could only possibly have an effect on fronzen samples which are exceedingly rare such as frozen wooly mammoths. However such external effects are not commonly seen. And as I mentioned, fossils that have undergone permineraliztion have essentially become rocks themselves and are immune to pretty much every effect unless you are talking about the sample being exposed and falling off into a volcano. ;D

Biochemist & Law Student

"The day will come when the mystical generation of Jesus, by the Supreme Being as His father, in the womb of a virgin will be classed with the fable of the generation of Minerva in the brain of Jupiter." -Thomas Jefferson

I got to admit, you guys keep coming up with answers that answer my questions quite well. This set of answers really exceeded my expectations. I thought that there would be some discrepancies described in the reliability of the many different data systems because I have heard criticisms of these different dating methods in theistic minded books. Although, from what you describe, the most reliable dating methods (I really liked the uranium - lead method) follow the scientific method very well. If there's a problem, gather more data to compare the problem data with. If there's still a problem, gather more data. I find the scientific testing method that you described very satisfying to know. Also, I do agree that identifying the age of rocks first, then inferring the age of trapped fossils seems quite reasonable indeed.

I just have two questions in response to your answers. First, How do scientists determine the margin of error for uranium lead dating? I understand the half-life bit, so I guess to refine my question further, how do chemists know the half-life of an isotope? I would love to hear what their inference mechanism is for determining such a range.

Secondly, can old rocks transfer their isotopes into the fossils within trapped within them? I apologize if this is an absurd question, but since the fossil can't change on its own, I wanted to know if it's possible that the rock could influence change on the fossil.

Again and again I will say it, thank you very much for your replies DewiMorgan and thraxas. I must know, what is your background in this field? Your replies are damn near academic instructional level sounding to my lehman ears. I would really love to read your replies and find out a little bit about your background. I don't want you to take this as an insult, a type of "checking your credentials." I have found every answer you've given me honest, clear, and as I see it truthful. There is no doubt in my mind of your reliability, I merely want to know how it is you came to acquire such an understanding of a broad range of science dealing with my questions. Thanks again, and I look forward to the replies.

The implication that we should put Darwinism on trial overlooks the fact that Darwinism has always been on trial within the scientific community. -- From Finding Darwin's God by Kenneth R. Miller

Chaos and chance don't mean the absence of law and order, but rather the presence of order so complex that it lies beyond our abilities to grasp and describe it. -- From From Certainty to Uncertainty by F. David Peat

Half life is determined experimentally. The experimental data is usually plugged into an equation after determing the decay constant and out pops the half life. Basically you have some starting amount of uranium isotope in the sample and you can set a certain amount of time for the experiment, and come back and see how much of the isotope has decayed. You can then extrapolate this to get half life. Half life basically means the amount of time it takes for half of the istopes in the sample to decay.

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Secondly, can old rocks transfer their isotopes into the fossils within trapped within them?

Nope. Almost all if not the totality of the isotopes we are looking at are particles that will decay and leave the rock as radiation. Meaning the isotopes either are deflected or go on through, they cannot lodge in something and not leave. For example, alpha radiation is deflected even by paper. Gamma rays which would literally destroy your organs would still pass right through you, so you would never relaly have any isotopes contaminating anything in the sense that you mean.

In terms of my background, I have a Ph.D. in biochemistry and molecular biology. I have also taken a lot of electives in geology and paleobiology. I am currently in law school. ;p

Biochemist & Law Student

"The day will come when the mystical generation of Jesus, by the Supreme Being as His father, in the womb of a virgin will be classed with the fable of the generation of Minerva in the brain of Jupiter." -Thomas Jefferson

Very interesting about the isotopes and gamma rays. Can you explain a little more about how it is they go right through us? Would then, the rays/isotopes go right through a fossil in the same way they go right through us?

The implication that we should put Darwinism on trial overlooks the fact that Darwinism has always been on trial within the scientific community. -- From Finding Darwin's God by Kenneth R. Miller

Chaos and chance don't mean the absence of law and order, but rather the presence of order so complex that it lies beyond our abilities to grasp and describe it. -- From From Certainty to Uncertainty by F. David Peat

Very interesting about the isotopes and gamma rays. Can you explain a little more about how it is they go right through us? Would then, the rays/isotopes go right through a fossil in the same way they go right through us?

Specifically, with the example of gamma rays - basically they are electromagnetic radiation produced from various sources such as from the sun or other types of radioactive decay. Essentially they are subatomic particles that are waves. Gamma rays have the highest energy of any radiation and has severe effects, so it would probably kill anyone exposed to it.

The way that all radiation behaves is that it they are waves (really wave and particle) that pass through things or are deflected by them depending on their energy and how thick and what it is that is deflecting. In the case of humans, the wave of a gamma ray will pass through a person and in the process destroy much of the DNA in their cells, it essential is a blast of energy that excites the phosphodiester bonds of DNA until they break. You have to think of radiation as transient energy, it is not something that can be really embedded in a person. It will only be eminanting at a steady pace from its source.

This works the same way with fossils and such. Gamma rays would pass right through a fossil without any change to it. Beta would likely be the same. Alpha radiation would be deflected by rock.

Biochemist & Law Student

"The day will come when the mystical generation of Jesus, by the Supreme Being as His father, in the womb of a virgin will be classed with the fable of the generation of Minerva in the brain of Jupiter." -Thomas Jefferson

My background is only as an interested layman: my grandma caused a bit of a stir in paleoanthro circles a few decades ago when she wrote a book called "The descent of woman", which made lots of people very cross by suggesting that maybe women were relevant for evolution as well, and possibly we had no hair because water was involved somewhere. So I've been into evolution all my life... which isn't that long, I'm only 32!

My degree is in electronics, and my career in computer programming, neither very relevant. Most of what I know I got from reading: with the help of back issues I've been reading the New Scientist magazine since the year I was born, which, along with SciAm, is probably where I picked up the worst wrong things

So, far more laymanesque than thraxas, who seems to really know his beans It's great to see someone like that going into law: there are far too few lawyers who know enough about science. Only the other day, we hear of a judge claiming not to know what a forum or a website was (in his defense, he may have been asking the question to ensure that this "technical point" was made clear to the jury).

Two nitpicks on points by thraxes: not so much wrong, as just clarifying the simplifications.

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Gamma rays have the highest energy of any radiation and has severe effects, so it would probably kill anyone exposed to it.

- hrm. They do have the highest energy of any EM radiation, being as how they are the high-frequency end of it. And they can and do cause cellular and genetic damage. But death would require a significant intensity. We are surrounded "background" levels of gamma radiation at all times.

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Basically you have some starting amount of uranium isotope in the sample and you can set a certain amount of time for the experiment, and come back and see how much of the isotope has decayed. You can then extrapolate this to get half life.

Since you normally never know how pure your original sample is, so you don't know how many atoms you have, you actually need to take measurements of decay over three periods, say over day one, day two and day three. Then look at the difference in decay rates. Say the first day was 4,000 clicks on your Geiger counter, and the second was 2,000, and the last 1,000. From that you can work out the half life (in this simple example, it's a day!)

One thing I find as I learn more is that most of the stuff I have been taught is either a lie that just will not die from the textbooks (the tongue taste map, the lemon battery, the spectrum-disc, the "sounds travel better through solids", the "raindrops have points", the 2-prism experiment, the seven colours of the rainbow, RYB as primary colours...), or is a simplification ("lies-to-children") of something far more complex.

This is well demonstrated with weight. As you learn, you get fed new lies:
1) Weight is constant
2) Weight isn't constant: mass is.
3) Mass isn't constant, but depends on velocity relative to lightspeed, which is constant.
4) Lightspeed isn't constant, and was much bigger earlier in the universe.
5) ???

...and so on. They're never deliberate lies, but it's often hard to establish exactly where the simplifications stop and the heavily argued hypotheses begin.

Incidentally, and slightly offtopically.... note that the mean lifetime of an atom isn't 2*halflife.

A lot of people seem to think that the fact that an atoms has a halflife means that it has an internal "clock" that counts down, saying "I'll fail at this time". They imagine a graph with a bell curve around the half life, showing when the atom is about to decay. And half the atoms in any sample have their clock set to that time, which happens to be *exactly* one half-life away from when you started measuring

But really, a half-life is just a way of saying "for every halflife length of time, T, you have a 50% chance of decaying sometime during that time". So the graph is flat, on whatever time scale you draw it on. In the above case, if you draw it on a graph with a scale of one day per square, it will be flat at 50%. At 12-hour squares it would be... 35-40%ish I think. With one second squares it would be a really tiny but constant chance of decaying each second.

So, with a bug clump of those atoms, in the first half-life, 50% of them have died (because they all had a 50-50 chance of dying). And in the next one, 50% of the remainder (because, still a 50% chance).

I tried to explain this flat probability graph thing to someone in another thread, and just confused them I think, so ignore me if I'm making no sense

Gamma rays have the highest energy of any radiation and has severe effects, so it would probably kill anyone exposed to it.

- hrm. They do have the highest energy of any EM radiation, being as how they are the high-frequency end of it. And they can and do cause cellular and genetic damage. But death would require a significant intensity. We are surrounded "background" levels of gamma radiation at all times.

Indeed, I was thinking more along the lines of getting a big blast of gamma rays from oh, a stellar body ;P ! lol

Biochemist & Law Student

"The day will come when the mystical generation of Jesus, by the Supreme Being as His father, in the womb of a virgin will be classed with the fable of the generation of Minerva in the brain of Jupiter." -Thomas Jefferson

I've reached a point where I don't have anymore good questions about this topic. I will say though that I have been doing a lot of reading during the day concerning this issue and others. I'm currently getting some great background dealing with evolution. In case you were wondering why I only post during the day and late at night it's because I work 6-11pm.

Don't fret though, I'll post up some new questions once I think of some.

The implication that we should put Darwinism on trial overlooks the fact that Darwinism has always been on trial within the scientific community. -- From Finding Darwin's God by Kenneth R. Miller

Chaos and chance don't mean the absence of law and order, but rather the presence of order so complex that it lies beyond our abilities to grasp and describe it. -- From From Certainty to Uncertainty by F. David Peat